Pulmonary lesions reshape swine respiratory microbiota: evidence of bacterial dysbiosis and reduced diversity.

The swine lower respiratory tract (LRT) microbiota has increasingly been investigated, but important knowledge gaps remain, limiting our understanding of microbial communities involved in respiratory health and disease. This longitudinal study evaluated the LRT bacterial composition of pigs with pulmonary lesions (PL+) compatible with Mycoplasma hyopneumoniae infection and without pulmonary lesions (PL-) across production phases from nursery to slaughter. Using 16 S-rRNA gene sequencing of intratracheal mucus and lung fragments, we observed longitudinal shifts in bacterial community composition. PL- animals showed higher observed richness and Shannon diversity during the finishing phases, whereas PL+ animals showed reduced alpha-diversity values and less pronounced temporal variation in relative composition. A total of 18 ASVs were detected across all sampled phases in both groups, suggesting a small set of persistent taxa; however, their prevalence, abundance, and ecological relevance remain unclear in the present analysis. Furthermore, LEfSe identified ASVs classified as Tetragenococcus halophilus and Bdellovibrio bacteriovorus as candidate discriminant taxa associated with PL + and PL- groups, respectively; these associations should be treated as preliminary and dataset-specific. Together, these findings suggest that pulmonary lesion status is associated with altered respiratory bacterial community patterns and support longitudinal approaches for investigating swine respiratory health.